During an interview with the Wall Street Journal, Ishihara had this to say:
“The NX is trying to change the concept of what it means to be a home console device or a hand-held device,” Ishihara said. “We will make games for the NX.”
While it is unclear whether the game will launch with the system, but we know it is coming and who will be working on it. Thanks to a report by MCV, we know that Game Freak will be making the Nintendo NX game; Game Freak being the developer of the hand-held version of the Pokemon games. With the Nintendo NX claiming to be a home console or a hand-held device, it would only make sense that Game Freak creates this Pokemon game; and possible give fans a true Pokemon game.